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Remove Dead Methods From gempyor.parameters.Parameters #414

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Remove Dead Methods From gempyor.parameters.Parameters #414

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53aa24f
Remove unused method from `Parameters`
TimothyWillard Dec 5, 2024
098e13d
Line length formatting
TimothyWillard Dec 5, 2024
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48 changes: 14 additions & 34 deletions flepimop/gempyor_pkg/src/gempyor/parameters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,8 @@ def __init__(
self.npar = len(self.pnames)
if self.npar != len(set([name.lower() for name in self.pnames])):
raise ValueError(
"Parameters of the SEIR model have the same name (remember that case is not sufficient!)"
"Parameters of the SEIR model have the same "
"name (remember that case is not sufficient!)"
)

# Attributes of dictionary
Expand Down Expand Up @@ -128,16 +129,18 @@ def __init__(
print("loaded dates:", df.index)
raise ValueError(
f"Issue loading file '{fn_name}' for parameter '{pn}': "
f"Provided file dates span '{str(df.index[0])}' to '{str(df.index[-1])}', "
f"but the config dates span '{ti}' to '{tf}'."
f"Provided file dates span '{str(df.index[0])}' to "
f"'{str(df.index[-1])}', but the config dates "
f"span '{ti}' to '{tf}'."
)
if not (pd.date_range(ti, tf) == df.index).all():
print("config dates:", pd.date_range(ti, tf))
print("loaded dates:", df.index)
raise ValueError(
f"Issue loading file '{fn_name}' for parameter '{pn}': "
f"Provided file dates span '{str(df.index[0])}' to '{str(df.index[-1])}', "
f"but the config dates span '{ti}' to '{tf}'."
f"Provided file dates span '{str(df.index[0])}' to "
f"'{str(df.index[-1])}', but the config dates "
f"span '{ti}' to '{tf}'."
)

self.pdata[pn]["ts"] = df
Expand All @@ -148,7 +151,8 @@ def __init__(
else:
self.pdata[pn]["stacked_modifier_method"] = "product"
logging.debug(
f"No 'stacked_modifier_method' for parameter {pn}, assuming multiplicative NPIs"
f"No 'stacked_modifier_method' for parameter {pn}, "
"assuming multiplicative NPIs."
)

if self.pconfig[pn]["rolling_mean_windows"].exists():
Expand All @@ -165,32 +169,6 @@ def __init__(
logging.debug(f"Index in arrays are: {self.pnames2pindex}")
logging.debug(f"NPI overlap operation is {self.stacked_modifier_method} ")

def picklable_lamda_alpha(self):
"""
Read the `alpha_val` attribute.

This defunct method returns the `alpha_val` attribute of this class which is
never set by this class. If this method is called and the `alpha_val` attribute
is not set an AttributeError will be raised.

Returns:
The `alpha_val` attribute.
"""
return self.alpha_val

def picklable_lamda_sigma(self):
"""
Read the `sigma_val` attribute.

This defunct method returns the `sigma_val` attribute of this class which is
never set by this class. If this method is called and the `sigma_val` attribute
is not set an AttributeError will be raised.

Returns:
The `sigma_val` attribute.
"""
return self.sigma_val

def get_pnames2pindex(self) -> dict:
"""
Read the `pnames2pindex` attribute.
Expand Down Expand Up @@ -235,7 +213,8 @@ class via `subpop_names`.
else:
param_arr[idx] = self.pdata[pn]["ts"].values

return param_arr # we don't store it as a member because this object needs to be small to be pickable
# we don't store it as a member because this object needs to be small to be pickable
return param_arr

def parameters_load(
self, param_df: pd.DataFrame, n_days: int, nsubpops: int
Expand Down Expand Up @@ -275,7 +254,8 @@ def parameters_load(
param_arr[idx] = self.pdata[pn]["ts"].values
else:
print(
f"PARAM: parameter {pn} NOT found in loadID file. Drawing from config distribution"
f"PARAM: parameter {pn} NOT found in loadID file. "
"Drawing from config distribution"
)
pval = self.pdata[pn]["dist"]()
param_arr[idx] = np.full((n_days, nsubpops), pval)
Expand Down
59 changes: 4 additions & 55 deletions flepimop/gempyor_pkg/tests/parameters/test_parameters_class.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@
import numpy as np
import pandas as pd
import pytest
from tempfile import NamedTemporaryFile

from gempyor.parameters import Parameters
from gempyor.testing import (
Expand Down Expand Up @@ -238,7 +237,8 @@ def test_timeseries_parameter_has_insufficient_columns_value_error(
ValueError,
match=(
rf"^Issue loading file '{tmp_file}' for parameter 'sigma': "
rf"the number of non-'date' columns is '{actual_columns}', expected '{mock_inputs.number_of_subpops()}' "
rf"the number of non-'date' columns is '{actual_columns}', expected "
rf"'{mock_inputs.number_of_subpops()}' "
rf"\(number of subpopulations\) or one\.$"
),
):
Expand Down Expand Up @@ -283,7 +283,8 @@ def test_timeseries_parameter_has_insufficient_dates_value_error(
ValueError,
match=(
f"Issue loading file '{tmp_file}' for parameter 'sigma': "
f"Provided file dates span '{timeseries_start_date}( 00:00:00)?' to '{timeseries_end_date}( 00:00:00)?', "
f"Provided file dates span '{timeseries_start_date}( 00:00:00)?' to "
rf"'{timeseries_end_date}( 00:00:00)?', "
f"but the config dates span '{mock_inputs.ti}' to '{mock_inputs.tf}'.$"
),
):
Expand Down Expand Up @@ -374,58 +375,6 @@ def test_parameters_instance_attributes(
expected_stacked_modifier_method[modifier_type].append(param_name.lower())
assert params.stacked_modifier_method == expected_stacked_modifier_method

@pytest.mark.parametrize(
"factory,alpha_val",
[
(fixed_three_valid_parameter_factory, None),
(fixed_three_valid_parameter_factory, 123),
(valid_parameters_factory, "abc"),
],
)
def test_picklable_lamda_alpha(
self,
tmp_path: pathlib.Path,
factory: Callable[[pathlib.Path], MockParametersInput],
alpha_val: Any,
) -> None:
# Setup
mock_inputs = factory(tmp_path)
params = mock_inputs.create_parameters_instance()

# Attribute error if `alpha_val` is not set
with pytest.raises(AttributeError):
params.picklable_lamda_alpha()

# We get the expected value when `alpha_val` is set
params.alpha_val = alpha_val
assert params.picklable_lamda_alpha() == alpha_val

@pytest.mark.parametrize(
"factory,sigma_val",
[
(fixed_three_valid_parameter_factory, None),
(fixed_three_valid_parameter_factory, 123),
(valid_parameters_factory, "abc"),
],
)
def test_picklable_lamda_sigma(
self,
tmp_path: pathlib.Path,
factory: Callable[[pathlib.Path], MockParametersInput],
sigma_val: Any,
) -> None:
# Setup
mock_inputs = factory(tmp_path)
params = mock_inputs.create_parameters_instance()

# Attribute error if `sigma_val` is not set
with pytest.raises(AttributeError):
params.picklable_lamda_sigma()

# We get the expected value when `sigma_val` is set
params.sigma_val = sigma_val
assert params.picklable_lamda_sigma() == sigma_val

@pytest.mark.parametrize(
"factory",
[
Expand Down
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